Ferredoxin



Ferredoxin (Fd) is found in chloroplasts which mediates electron transfer and contains an iron-sulfur cluster. It is involved in the photosynthesis process where its iron atoms accept or discharge electrons when they are being oxidized or reduced. The iron-sulfur cluster can contain 2Fe-2S and is termed plant-like or 3Fe-4S or 4Fe-4S clusters (e.g. 4Fe-4S Thermotoga maritima 1vjw to the right). Adrenodoxin (ADR) is a ferredoxin containing a 2Fe-2S group involved in electron transfer from NADPH+ to a cytochrome P-450 in the adrenal gland. Putidaredoxin (PUT) and terpredoxin (TER) are involved in the same reaction in bacteria and contain a 2Fe-2S group.



D14C variant of Pyrococcus furiosus ferredoxin
Structures of the all cysteinyl coordinated D14C variant of ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus have been determined for the [4Fe-4S] <-> and [3Fe-4S] forms (click to enlarge ). The [4Fe-4S] form diffracted to 1.7 Å and two different types of molecules were found in the crystal (2z8q). They have different crystal packing and intramolecular disulfide bond conformation. The crystal packing reveals a beta-sheet interaction between A molecules (shown in blue and green ) in adjacent asymmetric units, while B molecules are packed as monomers in a less rigid position next to the A-A extended beta-sheet dimers (shown in red and yellow ). The intramolecular disulfide bond in the A molecules is in a double conformation while the intramolecular disulfide bond in the B molecules is in a single conformation (click to see morph, molecule A is shown in blue and molecule B in green ).



Two forms of D14C [3Fe-4S] Pyrococcus furiosus ferredoxin are obtained when purified at pH 8.0: a monomer and a dimer connected by an intermolecular disulfide bond (see static image at the left). When purified at pH 5.8, only the monomer is obtained. The [3Fe-4S] form diffracted to 2.8 Å resolution and showed only the monomeric form, which resembles molecule A of D14C [4Fe-4S] Pyrococcus furiosus ferredoxin. Crystal packing in D14C [3Fe-4S] ferredoxin is as extended beta-sheet dimers of adjacent molecules (shown in red and orange ), which is the same as <scene name='Journal:JBIC:10/Cv2/9'>WT [3Fe-4S] P. furiosus ferredoxin (1sj1, shown in <font color='blue'>blue and <font color='cyan'>cyan ) even though the space groups are different (see also corresponding side views for <scene name='Journal:JBIC:10/Cv2/8'>D14C [3Fe-4S] ) and <scene name='Journal:JBIC:10/Cv2/10'>WT [3Fe-4S] ).

</StructureSection> <StructureSection load='1stp' size='500' side='right' scene='Journal:JBIC:12/Cv/2' caption=''>

ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004
Biological iron-sulfur (Fe-S) clusters are functionally versatile, modular prosthetic groups. The electronic structure and the site of iron reduction of these protein-bound cofactors account for the electron transfer function and mechanism. In the present work we have solved the structure of the ISC-like [2Fe-2S] ferredoxin called FdxB from the non-pathogenic gammaproteobacterium Pseudomonas putida JCM 20004 (formerly Pseudomonas ovalis IAM 1002). This FdxB protein contains an adrenodoxin (Adx) like, redox-active [2Fe-2S] cluster, which plays an essential role in the de novo iron-sulfur cluster assembly (ISC) system. It is encoded by the fdxB gene as a constituent of the cognate iscR-iscS1-iscU-iscA-hscB-hscA-fdxB gene cluster for the ISC system (DDBJ-EMBL-GenBank code AB109467). In P. putida the ISC pathway is apparently the sole system for in vivo Fe-S cluster assembly whereas the SUF pathway is missing in the bacterial genome (unlike in Escherichia coli).

The <scene name='Journal:JBIC:12/Cv1/1'>FdxB structure has a &#946;&#945;&#946;&#946;&#945;&#946; fold with the &#946;-grasp/ubiquitin-like fold motif as found in regular eukaryal and bacterial [2Fe-2S] ferredoxins (e.g. 1i7h, 1cje, 1e9m). FdxB is folded into an (&#945;+&#946;) <scene name='Journal:JBIC:12/Cv1/2'>core fold domain and an extended C-terminal tail. In the lattice <scene name='Journal:JBIC:12/Cv1/3'>FdxB was found to be homo-dimeric, displaying the <scene name='Journal:JBIC:12/Cv1/13'>isologous association of the extended C-terminal tail from each protomer. Each protomer binds a <scene name='Journal:JBIC:12/Cv1/4'>[2Fe-2S] cluster that is <scene name='Journal:JBIC:12/Cv1/5'>coordinated by four terminal cysteine sulfur atoms, where the <scene name='Journal:JBIC:12/Cv1/7'>outermost iron (Fe1) near the protein surface is coordinated by Cys41S and Cys47S and the <scene name='Journal:JBIC:12/Cv1/8'>innermost iron (Fe2) by Cys50S and Cys86S. In the <scene name='Journal:JBIC:12/Cv1/9'>dimeric structure, two [2Fe-2S] clusters are separated at the closest iron-to-iron (Fe1-Fe1) distance of 25 A, suggesting that a rapid interprotomer electron transfer between them would be unlikely to occur. In the place of the consensus free cysteine usually present near the [2Fe-2S] cluster of ISC-like ferredoxins, FdxB has the <scene name='Journal:JBIC:12/Cv1/10'>Lys45 side chain which forms a salt-bridge interaction with Asp65 O&#948;2. Thus, the overall FdxB structural features argue for its primarily electron transfer role in the cognate ISC system, rather than the direct catalytic function.

With the molecular structural frame determined from the FdxB structure, our electron-nuclear double resonance (ENDOR) analysis has allowed to determine the average gmax direction of the reduced FdxB, which is skewed, pointing roughly towards Cys50 C&#945; and forming an angle of about 27.3 (±4) degrees with the normal of the [2Fe-2S] plane, while the gint- and gmin-directions are distributed in a plane tilted toward the cluster plane (see image below). The site of reduced iron in the reduced FdxB is the outermost Fe1 site with the low negative spin density, while the innermost Fe2 site with the high positive spin population is the non-reducible iron retaining the Fe3+-valence of a reduced cluster. From a structural point of view, the larger number of polarized (or polarizable) bonds (NH, OH) and the <scene name='Journal:JBIC:12/Cv1/15'>extended hydrogen bonding network around Fe1 in FdxB may be the crucial factor favoring the accommodation of the reducing electron at the outermost Fe1 site. These results suggest a significant distortion of the electronic structure of the reduced [2Fe-2S] cluster under the influence of the protein environment around each iron site in general.

</StructureSection>

3D structures of ferredoxin
Update June 2011

2Fe-2S containing ferredoxins
2kaj, 1dox, 1doy – SyFd +Ga – Synechocystis – NMR

3hui – Fd – Rhodopseudomonas palustris

1off – SyFd

3gce – Fd – Nocardioides aromaticivorans

3lxf – Fd – Novosphingobium aromaticivorans

2e4p, 2e4q - Fd – Pseudomonas sp.

2q3w, 1vm9 - PmFd (mutant) – Pseudomonas mendocina

2i7f, 1uwm - RcFd – Rhodobacter capsulatus

1e9m – RcFd - NMR

1rfk, 3p63 - Fd – Cyanobacterium masticogladus laminosus

1vck - Fd – Pseudomonas resinovorans

1wri, 1frr - Fd – Equisetum arvense

1sjg - PmFd– NMR

1iue - Fd– Plasmodium falciparum

1m2a – AeFd – Aquifex aeolicus

1m2b, 1m2d, 1f37, 1f5b, 1f5c – AeFd (mutant)

1l5p – Fd – Trichomonas vaginalis

1i7h - Fd – Escherichia coli

1czp, 1qt9, 1frd, 1fxa - aFd– anabaena

1j7a, 1j7b, 1j7c, 1qoa, 1qob, 1qof, 1qog- aFd (mutant)

1e0z – Fd – Halobacterium salinarium

1pfd – Fd – Petroselinum crispum – NMR

1a70 - Fd (mutant) – Spinacia oleracea

1awd - Fd – Chlorella fusca

2cjn, 2cjo, 1roe – SyFd – NMR

1rof – SyFd – Synechococcus elongates

1doi - Fd – Haloarcula marismortui

4fxc – Fd – Spirulina platensis

1fxi – Fd – Aphanothece sacrum

3dqy, 2qpz, 3ah7]] - Fd – Pseudomonas putida

3ab5 – Fd – Cyanidioschyzon merolae

4Fe-4S containing ferredoxins
3eun – AvFd – Allochromatium vinosum

3exy - AvFd (mutant)

2vkr - Fd+Zn – Acidianus ambivalens

2z8q - PfFd (mutant) – Pyrococcus furiosus

1siz - PfFd 3pni - PfFd (mutant)

2fgo - Fd– Pseudomonas aeruginosa

1iqz, 1ir0 - BtFd  – Bacillus thermoproteolyticus

1rgv - Fd – Thauera aromatica

1dax, 1dfd – DaFd – Desulfovibrio africanus – NMR

1fxr - DaFd

1vjw – Fd – Thermotoga maritima

3Fe-4S containing ferredoxins
2v2k – Fd – Mycobacterium smegmatis

1wtf - BtFd (mutant)

1sj1 - PfFd

1fxd - DgFd – Desulfovibrio gigas

1f2g – DgFd – NMR

1xer - Fd – Sulfolobus tokodaii

4Fe-4S+3Fe-4S containing ferredoxins
1gao, 6fdr, 7fd1, 7fdr, 1axq, 6fd1, 1frh, 1fri,1frj, 1frk, 1frl, 1frm, 1fda, 1fdb, 1fdd, 5fd1, 1fer – AvFd – Azotobacter vinelandii

1pc4, 1pc5, 1g6b, 1g3o, 1ff2, 1b0v, 1d3w, 1b0t, 1a6l, 1ftc, 1frx, 2fd2, 1fd2 - AvFd (mutant)

1h98 – Fd – Thermus thermophilus

1a8p, 1bd6, 1bc6 - BsFd – Bacillus schlegelii – NMR

4Fe-4S+4Fe-4S containing ferredoxins
1dur – Fd – Peptoniphilus asaccarolyticus

1bwe, 1bqx - BsFd (mutant) – NMR

2fdn, 1fca, 1fdn- Fd – Clostridium acidi-urici

1blu - Fd – Chromatium vinosum

1clf – Fd – Clostridium pasteurianum – NMR

Adrenoredoxin
2jqr – ADR Fd domain (mutant)+cytochrome c (mutant) – yeast – NMR

2bt6 – cADR1 modified – cow

1l6u, 1l6v – cADR1 – NMR

1e6e – cADR (mutant)+ADR reductase

1cje, 1ayf - cADR

3na0 – hADR +cholesterol side-chain cleavage enzyme – human

3p1m - hADR

Putidaredoxin
1yji, 1yjj, 1pdx – PpPUT – NMR

3lb8 – PpPUT (mutant)+PUT reductase

1xln, 1xlo, 1xlp, 1xlq, 1r7s, 1oqq, 1oqr - PpPUT (mutant)

1gpx, 1put- PpPUT (mutant) - NMR

Terpredoxin
1b9r – TER – Pseudomonas - NMR